From: snoze pa (snoze.pa_at_gmail.com)
Date: Tue Apr 11 2006 - 14:48:12 CDT
I am trying to mutate ARG 5 to ALA and getting following message.
Warning: failed to set coordinate for atom CG ARG:5
Warning: failed to set coordinate for atom CD ARG:5
Warning: failed to set coordinate for atom NE ARG:5
Warning: failed to set coordinate for atom CZ ARG:5
Warning: failed to set coordinate for atom NH1 ARG:5
Warning: failed to set coordinate for atom NH2 ARG:5
I checked the output PDB and PSF files and it is clear that ARG5 is
replaced by ALA.
Despite of above message shall I assume that mutation to ALA is done
or there is some
problem with side chain? Here is sample
pdb and output.
Original PDB File
ATOM 38 N ARG 5 58.195 15.044 33.437 1.00 51.02
ATOM 39 CA ARG 5 58.492 14.011 32.450 1.00 51.51
ATOM 40 C ARG 5 57.305 13.098 32.223 1.00 51.03
ATOM 41 O ARG 5 56.915 12.832 31.089 1.00 50.19
ATOM 42 CB ARG 5 59.684 13.191 32.925 1.00 51.60
ATOM 43 CG ARG 5 60.754 14.046 33.569 1.00 52.60
ATOM 44 CD ARG 5 61.608 13.223 34.485 1.00 54.43
ATOM 45 NE ARG 5 62.697 12.616 33.753 1.00 56.67
ATOM 46 CZ ARG 5 63.796 13.268 33.407 1.00 57.48
ATOM 47 NH1 ARG 5 63.942 14.546 33.744 1.00 55.01
ATOM 48 NH2 ARG 5 64.734 12.641 32.710 1.00 57.01
Mutate PDB file
ATOM 66 N ALA 5 58.195 15.044 33.437 1.00 0.00
ATOM 67 HN ALA 5 58.900 15.191 34.130 0.00 0.00
ATOM 68 CA ALA 5 58.492 14.011 32.450 1.00 0.00
ATOM 69 HA ALA 5 58.720 14.461 31.490 0.00 0.00
ATOM 70 CB ALA 5 59.684 13.191 32.925 1.00 0.00
ATOM 71 HB1 ALA 5 60.568 13.853 33.044 0.00 0.00
ATOM 72 HB2 ALA 5 59.476 12.718 33.910 0.00 0.00
ATOM 73 HB3 ALA 5 59.948 12.393 32.198 0.00 0.00
ATOM 74 C ALA 5 57.305 13.098 32.223 1.00 0.00
ATOM 75 O ALA 5 56.915 12.832 31.089 1.00 0.00
Mutate PSF file
66 1B4C 59 ALA N NH1 -0.470000 14.0070 0
67 1B4C 59 ALA HN H 0.310000 1.0080 0
68 1B4C 59 ALA CA CT1 0.070000 12.0110 0
69 1B4C 59 ALA HA HB 0.090000 1.0080 0
70 1B4C 59 ALA CB CT3 -0.270000 12.0110 0
71 1B4C 59 ALA HB1 HA 0.090000 1.0080 0
72 1B4C 59 ALA HB2 HA 0.090000 1.0080 0
73 1B4C 59 ALA HB3 HA 0.090000 1.0080 0
74 1B4C 59 ALA C C 0.510000 12.0110 0
75 1B4C 59 ALA O O -0.510000 15.9990 0
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